The development of gene therapy and DNA vaccines has increased the demand for highly purified gene vectors such as plasmid DNA. The problem with the purification of supercoiled plasmid DNA is to completely remove other cell components such as host proteins, endotoxins, chromosomal DNA, RNA, open circular and nicked forms of plasmid DNA.
Different chromatographic methods have been used for plasmid DNA purification, such as size exclusion chromatography, or gel filtration, hydroxyapatite, ion exchange chromatography, reversed phase chromatography and hydrophobic interaction chromatography. Most of the methods lack the possibility to separate supercoiled plasmid DNA from other forms of the plasmid. Many of the available methods also use RNase to hydrolyse RNA in the cleared lysate before applying the sample to the chromatographic column. The usage of RNase is not recommendable in the preparation of plasmid DNA that is intended for human use.
Ion exchange chromatography is the most commonly used chromatography method. Plasmid DNA, chromosomal DNA and RNA all bind to anion exchangers as they have similar charge properties. Hydrophobic interaction chromatography has also been used, however, the plasmid DNA do not bind and was eluting in the flowthrough.